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PROSITE documentation PDOC51512 [for PROSITE entry PS51512]

DFDF domain and FFD and TFG boxes profiles





Description

Sm and Sm-like proteins of the RNA-binding Lsm (like Sm) domain family are found in all domains of life and are generally involved in important RNA-processing tasks. Lsm13-16 homologs share a domain organization consisting of a divergent N-terminal Lsm domain and a central or C-terminal consensus motif DFDF-x(7)-F closely preceded and followed by further phenylalanines and charged aspartates/glutamates and arginines/lysines/histidines. The variable seven-residue tract of this consensus motif usually contains an asparagine at the third or fourth position except of one sequence where the asparagine is replaced by a glycine. In few other sequences, the DFDF box is replaced by a DYDF or EFDF box [1]. The DFDF domain is a heterodimerization domain, which adopts a helical conformation upon binding (see <PDB:2WAX>). It folds into two consecutive α helices that are preceded and connected by the FDF and a related FDK sequence [2].

Two other strongly conserved FFD box and TFG box sequence motifs Y-x-K-x(3)-FFD-x-[IL]-S and [RKH]-x(2,5)-E-x(0-2)-[RK]-x(3,4)-[DE]-TFG contained in Lsm13-15, but not Lsm16, homologs succeed the DFDF-x(7)-F motif and are also predicted to be of helical nature [1].

The profiles we developed cover the entire DFDF domain and FFD and TFG boxes.

Last update:

May 2011 / First entry.

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Technical section

PROSITE methods (with tools and information) covered by this documentation:

DFDF, PS51512; DFDF domain profile  (MATRIX)

FFD, PS51513; FFD box profile  (MATRIX)

TFG, PS51536; TFG box profile  (MATRIX)


References

1AuthorsAlbrecht M. Lengauer T.
TitleNovel Sm-like proteins with long C-terminal tails and associated methyltransferases.
SourceFEBS Lett. 569:18-26(2004).
PubMed ID15225602
DOI10.1016/j.febslet.2004.03.126

2AuthorsTritschler F. Braun J.E. Eulalio A. Truffault V. Izaurralde E. Weichenrieder O.
TitleStructural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B.
SourceMol. Cell 33:661-668(2009).
PubMed ID19285948
DOI10.1016/j.molcel.2009.02.014



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